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| | <StructureSection load='4om8' size='340' side='right'caption='[[4om8]], [[Resolution|resolution]] 1.55Å' scene=''> | | <StructureSection load='4om8' size='340' side='right'caption='[[4om8]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4om8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_japonicum_(strain_lmg_29417_/_cect_9101_/_maff_303099) Mesorhizobium japonicum (strain lmg 29417 / cect 9101 / maff 303099)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OM8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4om8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OM8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mesorhizobium loti: mlr6793, mlr6793 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4om8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4om8 OCA], [https://pdbe.org/4om8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4om8 RCSB], [https://www.ebi.ac.uk/pdbsum/4om8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4om8 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4om8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4om8 OCA], [http://pdbe.org/4om8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4om8 RCSB], [http://www.ebi.ac.uk/pdbsum/4om8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4om8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/FHMCD_RHILO FHMCD_RHILO] Involved in the degradation of pyridoxine (vitamin B(6)). Catalyzes the oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate (FHMPC) by NAD(+) to 5-hydroxy-6-methylpyridine-3,4-dicarboxylate (HMPDC) (PubMed:19218190). Can also catalyze the reduction of FHMPC by NADH to 4-pyridoxic acid (PubMed:19218190).<ref>PMID:19218190</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kobayashi, J]] | + | [[Category: Mesorhizobium japonicum MAFF 303099]] |
| - | [[Category: Mikami, B]] | + | [[Category: Kobayashi J]] |
| - | [[Category: Mugo, A N]] | + | [[Category: Mikami B]] |
| - | [[Category: Ohnishi, K]] | + | [[Category: Mugo AN]] |
| - | [[Category: Yagi, T]] | + | [[Category: Ohnishi K]] |
| - | [[Category: Dehydrogenase]]
| + | [[Category: Yagi T]] |
| - | [[Category: Dismutase]]
| + | |
| - | [[Category: Enzyme function initiative]]
| + | |
| - | [[Category: Nad-binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| Structural highlights
Function
FHMCD_RHILO Involved in the degradation of pyridoxine (vitamin B(6)). Catalyzes the oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate (FHMPC) by NAD(+) to 5-hydroxy-6-methylpyridine-3,4-dicarboxylate (HMPDC) (PubMed:19218190). Can also catalyze the reduction of FHMPC by NADH to 4-pyridoxic acid (PubMed:19218190).[1]
Publication Abstract from PubMed
5-Formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase (FHMPCDH) from Mesorhizobium loti is the fifth enzyme in degradation pathway I for pyridoxine. The enzyme catalyzes a dismutation reaction: the oxidation of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) to 3-hydroxy-2-methylpyridine 4,5-dicarboxylic acid with NAD(+) and reduction of FHMPC to 4-pyridoxic acid with NADH. FHMPCDH belongs to the l-3-hydroxyacyl-CoA dehydrogenase (HAD) family. The crystal structure was determined by molecular replacement and refined to a resolution of 1.55A (R-factor of 16.4%, Rfree=19.4%). There were two monomers in the asymmetric unit. The overall structure of the monomer consisted of N- and C-terminal domains connected by a short linker loop. The monomer was similar to members of the HAD family (RMSD=1.9A). The active site was located between the domains and highly conserved to that of human heart l-3-hydroxyacyl-CoA dehydrogenase (HhHAD). His-Glu catalytic dyad, a serine and two asparagine residues of HhHAD were conserved. Ser116, His137 and Glu149 in FHMPCDH are connected by a hydrogen bonding network forming a catalytic triad. The functions of the active site residues in the reaction mechanism are discussed.
Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD(+)-dependent dismutase from Mesorhizobium loti.,Mugo AN, Kobayashi J, Mikami B, Yoshikane Y, Yagi T, Ohnishi K Biochem Biophys Res Commun. 2015 Jan 2;456(1):35-40. doi:, 10.1016/j.bbrc.2014.11.028. Epub 2014 Nov 18. PMID:25446130[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yokochi N, Yoshikane Y, Matsumoto S, Fujisawa M, Ohnishi K, Yagi T. Gene identification and characterization of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD+-dependent dismutase. J Biochem. 2009 Apr;145(4):493-503. doi: 10.1093/jb/mvp007. Epub 2009 Jan 17. PMID:19218190 doi:http://dx.doi.org/10.1093/jb/mvp007
- ↑ Mugo AN, Kobayashi J, Mikami B, Yoshikane Y, Yagi T, Ohnishi K. Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD(+)-dependent dismutase from Mesorhizobium loti. Biochem Biophys Res Commun. 2015 Jan 2;456(1):35-40. doi:, 10.1016/j.bbrc.2014.11.028. Epub 2014 Nov 18. PMID:25446130 doi:http://dx.doi.org/10.1016/j.bbrc.2014.11.028
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